Re: [HCP-Users] MSMAll Failure Following hcp-fix_multi-run

[Glasser, Matthew]

Please upgrade to the latest version of the HCP Pipelines (the latest master 
has a few fixes relative to 4.0.0), the latest FSL 6.0.1, and the latest FIX.

Matt.

From:  on behalf of Timothy Hendrickson 

Date: Sunday, June 23, 2019 at 4:32 PM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] MSMAll Failure Following hcp-fix_multi-run

Hello,

I am having issues running MSMAll following hcp-fix_multi-run for a study that 
I am doing processing for. The particular study that I am processing data for 
has 6 fMRI scans totalling 2950 timepoints per scanning session. I am certainly 
aware of the large amount of memory that hcp-fix_multi-run requires as it is 
fed more timepoints, however, this is completing without issue. I am running 
HCP version 3.27.0 with MSMAll v2 and FSL 5.0.11.

Is there a way to get around this error?
If I end up having to break up hcp-fix_multi-run do you have any best practices 
on how to do this (i.e. should it be a mix of tfMRI and rsfMRI, etc)?

Best,

-Tim
Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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[HCP-Users] MSMAll Failure Following hcp-fix_multi-run

[Timothy Hendrickson]

Hello,

I am having issues running MSMAll following hcp-fix_multi-run for a study
that I am doing processing for. The particular study that I am processing
data for has 6 fMRI scans totalling 2950 timepoints per scanning session. I
am certainly aware of the large amount of memory that hcp-fix_multi-run
requires as it is fed more timepoints, however, this is completing without
issue. I am running HCP version 3.27.0 with MSMAll v2 and FSL 5.0.11.

Is there a way to get around this error?
If I end up having to break up hcp-fix_multi-run do you have any best
practices on how to do this (i.e. should it be a mix of tfMRI and rsfMRI,
etc)?

Best,

-Tim
Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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HCP-Users@humanconnectome.org
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Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Glasser, Matthew]

MSMAll is supposed to have higher distortions than MSMSulc.  This is by design 
as we are very conservative about distortions with MSMSulc to avoid overfitting 
to folds (a rampant problem in both folding-based surface registration and 
volume-based registration).  Whether MSMAll was working is not determined 
solely by the distortions, but rather their magnitude with respect to known 
good data, the quality of the alignment itself, and the test-retest 
reproducibility of the alignment.

Matt.

From: Maria Sison 
Date: Friday, May 10, 2019 at 3:15 PM
To: "Glasser, Matthew" , "Harms, Michael" 
, Steve Smith 
Cc: HCP 讨论组 
Subject: RE: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you for all of the insightful comments, this has been a huge help. I 
think we’ll stick with MSMSulc measures until we have a clearer idea of what 
data we’d need to confidently run MSMAll. I compared strain maps for MSMSulc 
and MSMAll and in general the values are more extreme for MSMAll. I also made 
maps of areal distortion (-surface-distortion) between test and retest MSMAll 
midthickness and these were more extreme across the whole cortex when compared 
to MSMSulc test retest distortion maps, so this seems to line up with what 
Michael was saying about our MSMAll registrations.

Best,
Maria


From: Glasser, Matthew 
Sent: Thursday, May 9, 2019 9:22:51 PM
To: Harms, Michael; Maria Sison; Steve Smith
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

This issue of what kind of data and how much is something we plan to 
investigate in detail for MSMAll (and the cortical areal classifier).

Matt.

From: "Harms, Michael" 
Date: Thursday, May 9, 2019 at 4:41 PM
To: "Glasser, Matthew" , Maria Sison 
, Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data


While I’m not surprised that the ICCs would be lower for an anatomical-based 
measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change 
(from 0.9 to 0.65), especially for a parcellated analysis, since only changes 
in the precise border of the parcellations should be affecting the results.

Your results imply that the test and retest MSMAll registrations are very 
different from each other.

Wouldn’t the Strain maps for MSMSulc vs MSMAll be informative here?  You might 
also want to examine some sort of measure of the distortion between the two 
MSMAll registrations directly.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Glasser, Matthew" 

Date: Thursday, May 9, 2019 at 4:23 PM
To: Maria Sison , Stephen Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Not running sICA+FIX might well be a part of the problem.  The TR is quite long 
as Steve says, which will limit the accuracy of sICA+FIX cleanup some also.  
Also, surface area and thickness might prefer MSMSulc due to correlations with 
folding patterns.  Myelin, task, and resting state fMRI will more tend to 
correlate with MSMAll.

Matt.

From:  on behalf of Maria Sison 

Date: Thursday, May 9, 2019 at 3:40 PM
To: Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.










On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Maria Sison]

Thank you for all of the insightful comments, this has been a huge help. I 
think we’ll stick with MSMSulc measures until we have a clearer idea of what 
data we’d need to confidently run MSMAll. I compared strain maps for MSMSulc 
and MSMAll and in general the values are more extreme for MSMAll. I also made 
maps of areal distortion (-surface-distortion) between test and retest MSMAll 
midthickness and these were more extreme across the whole cortex when compared 
to MSMSulc test retest distortion maps, so this seems to line up with what 
Michael was saying about our MSMAll registrations.

Best,
Maria


From: Glasser, Matthew 
Sent: Thursday, May 9, 2019 9:22:51 PM
To: Harms, Michael; Maria Sison; Steve Smith
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

This issue of what kind of data and how much is something we plan to 
investigate in detail for MSMAll (and the cortical areal classifier).

Matt.

From: "Harms, Michael" 
Date: Thursday, May 9, 2019 at 4:41 PM
To: "Glasser, Matthew" , Maria Sison 
, Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data


While I’m not surprised that the ICCs would be lower for an anatomical-based 
measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change 
(from 0.9 to 0.65), especially for a parcellated analysis, since only changes 
in the precise border of the parcellations should be affecting the results.

Your results imply that the test and retest MSMAll registrations are very 
different from each other.

Wouldn’t the Strain maps for MSMSulc vs MSMAll be informative here?  You might 
also want to examine some sort of measure of the distortion between the two 
MSMAll registrations directly.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Glasser, Matthew" 

Date: Thursday, May 9, 2019 at 4:23 PM
To: Maria Sison , Stephen Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Not running sICA+FIX might well be a part of the problem.  The TR is quite long 
as Steve says, which will limit the accuracy of sICA+FIX cleanup some also.  
Also, surface area and thickness might prefer MSMSulc due to correlations with 
folding patterns.  Myelin, task, and resting state fMRI will more tend to 
correlate with MSMAll.

Matt.

From:  on behalf of Maria Sison 

Date: Thursday, May 9, 2019 at 3:40 PM
To: Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.









On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
d

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Glasser, Matthew]

This issue of what kind of data and how much is something we plan to 
investigate in detail for MSMAll (and the cortical areal classifier).

Matt.

From: "Harms, Michael" 
Date: Thursday, May 9, 2019 at 4:41 PM
To: "Glasser, Matthew" , Maria Sison 
, Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data


While I’m not surprised that the ICCs would be lower for an anatomical-based 
measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change 
(from 0.9 to 0.65), especially for a parcellated analysis, since only changes 
in the precise border of the parcellations should be affecting the results.

Your results imply that the test and retest MSMAll registrations are very 
different from each other.

Wouldn’t the Strain maps for MSMSulc vs MSMAll be informative here?  You might 
also want to examine some sort of measure of the distortion between the two 
MSMAll registrations directly.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Glasser, Matthew" 

Date: Thursday, May 9, 2019 at 4:23 PM
To: Maria Sison , Stephen Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Not running sICA+FIX might well be a part of the problem.  The TR is quite long 
as Steve says, which will limit the accuracy of sICA+FIX cleanup some also.  
Also, surface area and thickness might prefer MSMSulc due to correlations with 
folding patterns.  Myelin, task, and resting state fMRI will more tend to 
correlate with MSMAll.

Matt.

From:  on behalf of Maria Sison 

Date: Thursday, May 9, 2019 at 3:40 PM
To: Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.









On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.






On 9 May 2019, at 14:45, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar t

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Harms, Michael]

While I’m not surprised that the ICCs would be lower for an anatomical-based 
measure for MSMAll than MSMSulc, I am surprised by the magnitude of the change 
(from 0.9 to 0.65), especially for a parcellated analysis, since only changes 
in the precise border of the parcellations should be affecting the results.

Your results imply that the test and retest MSMAll registrations are very 
different from each other.

Wouldn’t the Strain maps for MSMSulc vs MSMAll be informative here?  You might 
also want to examine some sort of measure of the distortion between the two 
MSMAll registrations directly.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110  Email: mha...@wustl.edu

From:  on behalf of "Glasser, Matthew" 

Date: Thursday, May 9, 2019 at 4:23 PM
To: Maria Sison , Stephen Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Not running sICA+FIX might well be a part of the problem.  The TR is quite long 
as Steve says, which will limit the accuracy of sICA+FIX cleanup some also.  
Also, surface area and thickness might prefer MSMSulc due to correlations with 
folding patterns.  Myelin, task, and resting state fMRI will more tend to 
correlate with MSMAll.

Matt.

From:  on behalf of Maria Sison 

Date: Thursday, May 9, 2019 at 3:40 PM
To: Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.








On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.





On 9 May 2019, at 14:45, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar to those for 
MSMSulc (both above 0.9), but still slightly lower.

There are a few major differences in how we ran the pipeline. We skipped 
sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
but before fMRISulc (bandpass filtering, motion correction, censoring, 
CompCorr, and regressed out tasks). We thought our processing would be ok for 
c

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Glasser, Matthew]

Not running sICA+FIX might well be a part of the problem.  The TR is quite long 
as Steve says, which will limit the accuracy of sICA+FIX cleanup some also.  
Also, surface area and thickness might prefer MSMSulc due to correlations with 
folding patterns.  Myelin, task, and resting state fMRI will more tend to 
correlate with MSMAll.

Matt.

From:  on behalf of Maria Sison 

Date: Thursday, May 9, 2019 at 3:40 PM
To: Steve Smith 
Cc: HCP 讨论组 
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.







On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.




On 9 May 2019, at 14:45, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar to those for 
MSMSulc (both above 0.9), but still slightly lower.

There are a few major differences in how we ran the pipeline. We skipped 
sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
but before fMRISulc (bandpass filtering, motion correction, censoring, 
CompCorr, and regressed out tasks). We thought our processing would be ok for 
cleaning task fMRI, but I see that sICA+FIX is highly recommended before 
running MSMAll 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg06876.html=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=owCDH48LPtiA_trirzvrgF5FPS8Ba-Yz0KyPbwHJ6Mc=>),
 so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so 
dependent on sICA+FIX that it could be causing these problems in our data or do 
you have any other ideas about why we're getting such a large drop in ICCs for 
MSMAll? In other words, what are the minimal preprocessing requirements to 
effectively use MSMAll in non-HCP data? Any comments would be appreciated!

Thank you,
Maria
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Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Maria Sison]

Thank you so much, this is very helpful and interesting to think about. We 
concatenated rest and tasks and regressed out tasks to get around 1000 TRs of 
pseudo-rest which we then used for MSMAll. Still not nearly as much as HCP, but 
I would be interested to hear what a ballpark minimum data requirement for 
MSMALL would be.

Best,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 4:19:24 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.






On 9 May 2019, at 15:12, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.



On 9 May 2019, at 14:45, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar to those for 
MSMSulc (both above 0.9), but still slightly lower.

There are a few major differences in how we ran the pipeline. We skipped 
sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
but before fMRISulc (bandpass filtering, motion correction, censoring, 
CompCorr, and regressed out tasks). We thought our processing would be ok for 
cleaning task fMRI, but I see that sICA+FIX is highly recommended before 
running MSMAll 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg06876.html=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=owCDH48LPtiA_trirzvrgF5FPS8Ba-Yz0KyPbwHJ6Mc=>),
 so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so 
dependent on sICA+FIX that it could be causing these problems in our data or do 
you have any other ideas about why we're getting such a large drop in ICCs for 
MSMAll? In other words, what are the minimal preprocessing requirements to 
effectively use MSMAll in non-HCP data? Any comments would be appreciated!

Thank you,
Maria

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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.uk&l

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Steve Smith]

Hi - probably the single primary thing is number of timepoints - though things 
like TR and spatial resolution will also affect this.

My guess is still that probably you don't have enough timepoints here to get 
decent single-subject RSN maps (decen enough for MSMALL that is).  Emma or Matt 
might have more direct insight into the minimum amount of data you need to get 
MSMALL working well.   Unless you can combine more of your datasets together 
(even if just for the purposes of MSM) then you might be better off with 
MSMSULC.

Cheers.

ps with this setup I would definitely push multiband at least as high as 6 if 
not 8.






> On 9 May 2019, at 15:12, Maria Sison  wrote:
> 
> Hello,
>  
> Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
> 3T scanner equipped with a 64-channel head/neck coil. A series of 72 
> interleaved axial T2-weighted functional slices were acquired using a 3-fold 
> multi-band accelerated echo planar imaging sequence with the following 
> parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
> mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total 
> scan length is 496 s.
>  
> Out of curiosity, which parameters would be most important for MSMAll?
>  
> Thank you,
> Maria
>  
> From: Steve Smith mailto:st...@fmrib.ox.ac.uk>>
> Sent: Thursday, May 9, 2019 3:56:49 PM
> To: Maria Sison
> Cc: HCP 讨论组
> Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data
>  
> Hi - what is your rfMRI protocol?   It might be that you're right that the 
> difference is in the preprop - but my first guess might be that - if the 
> rfMRI data is not as high quality as HCP rfMRI data - it might not be good 
> enough to reliably drive MSMALL?
> 
> Cheers.
> 
> 
> 
>> On 9 May 2019, at 14:45, Maria Sison > <mailto:maria.si...@duke.edu>> wrote:
>> 
>> Dear experts,
>>  
>> We have run the HCP minimal preprocessing pipelines on our data (1 mm 
>> isotropic T1w and FLAIR + rest and 4 tasks) and compared test-retest 
>> reliability for MSMSulc and MSMAll in 20 subjects. Specifically, we looked 
>> at intraclass correlations for parcellated cortical thickness and surface 
>> area and found that they were much lower for MSMAll compared to MSMSulc in 
>> our test-retest sample (MSMSulc on average above 0.9 and for MSMAll around 
>> 0.65 on average). When we looked in HCP retest data, the ICCs for MSMAll 
>> were more similar to those for MSMSulc (both above 0.9), but still slightly 
>> lower. 
>>  
>> There are a few major differences in how we ran the pipeline. We skipped 
>> sICA+FIX and ran our own preprocessing on task and rest fMRI after 
>> fMRIVolume but before fMRISulc (bandpass filtering, motion correction, 
>> censoring, CompCorr, and regressed out tasks). We thought our processing 
>> would be ok for cleaning task fMRI, but I see that sICA+FIX is highly 
>> recommended before running MSMAll 
>> (https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html 
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg06876.html=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=owCDH48LPtiA_trirzvrgF5FPS8Ba-Yz0KyPbwHJ6Mc=>),
>>  so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is 
>> so dependent on sICA+FIX that it could be causing these problems in our data 
>> or do you have any other ideas about why we're getting such a large drop in 
>> ICCs for MSMAll? In other words, what are the minimal preprocessing 
>> requirements to effectively use MSMAll in non-HCP data? Any comments would 
>> be appreciated!
>>  
>> Thank you,
>> Maria
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=5J6HdZ4Fo_r3ENfbGzf9A5NOjDXu5D5DCwt8ZS8HkVg=>
> 
> ---
> Stephen M. Smith, Professor of Biomedical Engineering
> Head of Analysis,  WIN (FMRIB) Oxford
> 
> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
> +44 (0) 1865 610470
> st...@fmrib.ox.ac.uk <mailto:st...@fmrib.ox.ac.uk>
> http://www.fmrib.ox.a

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Maria Sison]

Hello,

Here’s our rfMRI protocol: each participant was scanned using a Siemens Skyra 
3T scanner equipped with a 64-channel head/neck coil. A series of 72 
interleaved axial T2-weighted functional slices were acquired using a 3-fold 
multi-band accelerated echo planar imaging sequence with the following 
parameters: TR = 2000 ms, TE = 27 msec, flip angle = 90°, field-of-view = 200 
mm, voxel size = 2 mm isotropic, slice thickness = 2 mm without gap. Total scan 
length is 496 s.

Out of curiosity, which parameters would be most important for MSMAll?

Thank you,
Maria


From: Steve Smith 
Sent: Thursday, May 9, 2019 3:56:49 PM
To: Maria Sison
Cc: HCP 讨论组
Subject: Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.



On 9 May 2019, at 14:45, Maria Sison 
mailto:maria.si...@duke.edu>> wrote:

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar to those for 
MSMSulc (both above 0.9), but still slightly lower.

There are a few major differences in how we ran the pipeline. We skipped 
sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
but before fMRISulc (bandpass filtering, motion correction, censoring, 
CompCorr, and regressed out tasks). We thought our processing would be ok for 
cleaning task fMRI, but I see that sICA+FIX is highly recommended before 
running MSMAll 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_hcp-2Dusers-40humanconnectome.org_msg06876.html=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=owCDH48LPtiA_trirzvrgF5FPS8Ba-Yz0KyPbwHJ6Mc=>),
 so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so 
dependent on sICA+FIX that it could be causing these problems in our data or do 
you have any other ideas about why we're getting such a large drop in ICCs for 
MSMAll? In other words, what are the minimal preprocessing requirements to 
effectively use MSMAll in non-HCP data? Any comments would be appreciated!

Thank you,
Maria

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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>
http://www.fmrib.ox.ac.uk/~steve<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fmrib.ox.ac.uk_-7Esteve=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=flsdWLpWURamBFUowb_0CPPOb_320ohP4cEZWX9OfmQ=>
---

Stop the cultural destruction of 
Tibet<https://urldefense.proofpoint.com/v2/url?u=http-3A__smithinks.net=DwMFaQ=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc=jYoYbUrDg7XpYyosGa9JK-bzhv9_497jTGvkuIGUvC4=L2sucJXfwykaL3uBceFg9ItkjPLvmDK9C4reZWm3I3w=YgiVdNVcsd8Q5XdU8ruCngYSzvnnxWMf0PaRuPdVRRI=>









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Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Steve Smith]

Hi - what is your rfMRI protocol?   It might be that you're right that the 
difference is in the preprop - but my first guess might be that - if the rfMRI 
data is not as high quality as HCP rfMRI data - it might not be good enough to 
reliably drive MSMALL?

Cheers.



> On 9 May 2019, at 14:45, Maria Sison  wrote:
> 
> Dear experts,
>  
> We have run the HCP minimal preprocessing pipelines on our data (1 mm 
> isotropic T1w and FLAIR + rest and 4 tasks) and compared test-retest 
> reliability for MSMSulc and MSMAll in 20 subjects. Specifically, we looked at 
> intraclass correlations for parcellated cortical thickness and surface area 
> and found that they were much lower for MSMAll compared to MSMSulc in our 
> test-retest sample (MSMSulc on average above 0.9 and for MSMAll around 0.65 
> on average). When we looked in HCP retest data, the ICCs for MSMAll were more 
> similar to those for MSMSulc (both above 0.9), but still slightly lower. 
>  
> There are a few major differences in how we ran the pipeline. We skipped 
> sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
> but before fMRISulc (bandpass filtering, motion correction, censoring, 
> CompCorr, and regressed out tasks). We thought our processing would be ok for 
> cleaning task fMRI, but I see that sICA+FIX is highly recommended before 
> running MSMAll 
> (https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html 
> ), 
> so I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so 
> dependent on sICA+FIX that it could be causing these problems in our data or 
> do you have any other ideas about why we're getting such a large drop in ICCs 
> for MSMAll? In other words, what are the minimal preprocessing requirements 
> to effectively use MSMAll in non-HCP data? Any comments would be appreciated!
>  
> Thank you,
> Maria
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org 
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> 

---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  WIN (FMRIB) Oxford

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 610470
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 









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[HCP-Users] MSMAll vs. MSMSulc reliability in our data

[Maria Sison]

Dear experts,

We have run the HCP minimal preprocessing pipelines on our data (1 mm isotropic 
T1w and FLAIR + rest and 4 tasks) and compared test-retest reliability for 
MSMSulc and MSMAll in 20 subjects. Specifically, we looked at intraclass 
correlations for parcellated cortical thickness and surface area and found that 
they were much lower for MSMAll compared to MSMSulc in our test-retest sample 
(MSMSulc on average above 0.9 and for MSMAll around 0.65 on average). When we 
looked in HCP retest data, the ICCs for MSMAll were more similar to those for 
MSMSulc (both above 0.9), but still slightly lower.

There are a few major differences in how we ran the pipeline. We skipped 
sICA+FIX and ran our own preprocessing on task and rest fMRI after fMRIVolume 
but before fMRISulc (bandpass filtering, motion correction, censoring, 
CompCorr, and regressed out tasks). We thought our processing would be ok for 
cleaning task fMRI, but I see that sICA+FIX is highly recommended before 
running MSMAll 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06876.html), so 
I’m planning to try to rerun with sICA+FIX. Do you think that MSMAll is so 
dependent on sICA+FIX that it could be causing these problems in our data or do 
you have any other ideas about why we're getting such a large drop in ICCs for 
MSMAll? In other words, what are the minimal preprocessing requirements to 
effectively use MSMAll in non-HCP data? Any comments would be appreciated!

Thank you,
Maria

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Re: [HCP-Users] MSMAll, missing _vn file

[Glasser, Matthew]

This issue will be resolved in the upcoming MR+FIX release.  There is no simple 
workaround.

Matt.


Sent from my Verizon, Samsung Galaxy smartphone


 Original message 
From: Marta Moreno 
Date: 3/4/19 10:30 AM (GMT-06:00)
To: HCP Users 
Subject: [HCP-Users] MSMAll, missing _vn file

Dear experts,

I am running MSMAllPipelineBatch.sh after hcp_fix on a 10min run (rsfMRI) and 
getting an error saying that the file: 
"RS_fMRI_1_Atlas_hp2000_clean_vn_tempcompute.dscalar.nii" does not exist. I am 
using fsl 5.0.11 and fix 1.067.

Any help?

Thanks,

Leah






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The materials in this message are private and may contain Protected Healthcare 
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intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
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[HCP-Users] MSMAll, missing _vn file

[Marta Moreno]

Dear experts,

I am running MSMAllPipelineBatch.sh after hcp_fix on a 10min run (rsfMRI) and 
getting an error saying that the file: 
"RS_fMRI_1_Atlas_hp2000_clean_vn_tempcompute.dscalar.nii" does not exist. I am 
using fsl 5.0.11 and fix 1.067. 

Any help?

Thanks,

Leah






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Re: [HCP-Users] MSMAll

[Glasser, Matthew]

MSMAll is aligned to fs_LR.  I believe there are instructions on the HCP FAQ to 
get to fsaverage space, though you could also just downsample in fs_LR space by 
creating a less dense spheres with wb_command -surface-create-sphere, following 
the instructions in the usage and then using wb_command -cifti-resample.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Bai Haohao mailto:jarblank1...@gmail.com>>
Date: Tuesday, December 25, 2018 at 8:04 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Dear HCP users,

I am using Movie Task fMRI 2mm/32k FIX-Denoised (Compact), and I found MSMALL 
in one file's name, but not found fs_LR in any file's name.

I wonder whether can I simply understand MSMALL file as registered to fs_LR 
mesh? Or still in individual space?

Can I just project the MSMAll data to fsaverage5 space(for quicker compute) 
with wb_command through the fs_LR group data to fsaverage way?

Thanks in advance,

Haohao Bai

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The materials in this message are private and may contain Protected Healthcare 
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[HCP-Users] MSMAll

[Bai Haohao]

Dear HCP users,

I am using *Movie Task fMRI 2mm/32k FIX-Denoised (Compact), *and I found MSMALL
in one file's name, but not found fs_LR in any file's name.

I wonder whether can I simply understand MSMALL file as registered to fs_LR
mesh? Or still in individual space?

Can I just project the MSMAll data to fsaverage5 space(for quicker compute)
with wb_command through the *fs_LR group data to fsaverage* way?

Thanks in advance,

Haohao Bai

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Re: [HCP-Users] MSMall Question

[Glasser, Matthew]

There is no specific cost function weighting being used (i.e. each feature has 
the same weight).

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Curtis, Mark T" mailto:mac...@pitt.edu>>
Date: Monday, November 5, 2018 at 4:52 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMall Question

Hello,

I have a question about MSMall, as I am trying to better understand how it is 
performing the alignment in the HCP Pipelines. My understanding is that MSMall 
uses areal features that include myelin maps and resting state network maps for 
alignment. MSM uses a discrete optimization approach and optimizes across the 
surface until features on the moving surface best match the target surface and 
it does this over a series of iterations. In the HCP Pipelines, how is this 
being done for the different modalities? Is it doing it for each modality on 
its own or is it creating a single, multivariate CostFunctionweighted mask and 
using it as the –refweight option? If it’s the latter, what are the actual 
weights that are used as default in the pipeline for the different modalities?

Any help with my understanding is appreciated!

Thanks!
Mark


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[HCP-Users] MSMall Question

[Curtis, Mark T]

Hello,

I have a question about MSMall, as I am trying to better understand how it is 
performing the alignment in the HCP Pipelines. My understanding is that MSMall 
uses areal features that include myelin maps and resting state network maps for 
alignment. MSM uses a discrete optimization approach and optimizes across the 
surface until features on the moving surface best match the target surface and 
it does this over a series of iterations. In the HCP Pipelines, how is this 
being done for the different modalities? Is it doing it for each modality on 
its own or is it creating a single, multivariate CostFunctionweighted mask and 
using it as the –refweight option? If it’s the latter, what are the actual 
weights that are used as default in the pipeline for the different modalities?

Any help with my understanding is appreciated!

Thanks!
Mark


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Re: [HCP-Users] MSMAll for MultiRunICAFIX

[Glasser, Matthew]

Watch this space for an update on MSMAll with MultiRunFIX.  The pipelines
in the current master aren¹t all working together and we are working on
fixing that.

Matt.

On 10/9/18, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim"  wrote:

>Dear Experts:
>
>I have a question for MSMAll alignment for MultiRunICAFIX cleaned data.
>Once I run the MultiRunICAFIX pipeline, I get the output like
>"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii".
>
>But I want to align the data (e.g.,
>${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii) using MSMAll pipeline.
>Running MSMAllPipeline script with above data seems to be fine without
>any error. However, if I run DeDriftAndResamplePipeline script,
>it requires ${fMRIConcatName}.${Hemisphere}.native.func.gii, which is
>absent in ${fMRIConcatName} folder.
>
>I can generate ${fMRIConcatName}.${Hemisphere}.native.func.gii using
>fMRISurfacePipeline.
>But I¹m just wondering that I should run fMRISurfacePipeline for
>MultiRunICAFIX-cleaned data.
>
>This might be silly question as I don¹t clearly understand MSMAllPipeline
>and DeDriftAndResamplePipeline.
>Is there a method to have MSMAll-aligned MultiRunICAFIX-cleaned data?
>
>Below is the scripts that I ran:
>
>## MultiRunICAFIX
>StudyFolder="/Volumes/easystore/projects/HCP"
>Subject="300"
>ConcatName1="rfMRI_REST_Concat_Day1"
>ConcatName2="rfMRI_REST_Concat_Day2"
>ResultFolder="${StudyFolder}/${Subject}/MNINonlinear/Results"
>ICAFIXscriptFolder="/Users/sang-young/projects/Pipelines_master/ICAFIX"
>
>${ICAFIXscriptFolder}/hcp_fix_multi_run
>${ResultFolder}/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz@${ResultFolder}/rfMRI
>_REST1_PA/rfMRI_REST1_PA.nii.gz@${ResultFolder}/rfMRI_REST2_AP/rfMRI_REST2
>_AP.nii.gz@${ResultFolder}/rfMRI_REST2_PA/rfMRI_REST2_PA.nii.gz 2000
>${ResultFolder}/${ConcatName1}/${ConcatName1}.nii.gz
>${FSL_FIXDIR}/training_files/HCP_hp2000.RData
>
>${ICAFIXscriptFolder}/hcp_fix_multi_run
>${ResultFolder}/rfMRI_REST3_AP/rfMRI_REST3_AP.nii.gz@${ResultFolder}/rfMRI
>_REST3_PA/rfMRI_REST3_PA.nii.gz@${ResultFolder}/rfMRI_REST4_AP/rfMRI_REST4
>_AP.nii.gz@${ResultFolder}/rfMRI_REST4_PA/rfMRI_REST4_PA.nii.gz 2000
>${ResultFolder}/${ConcatName2}/${ConcatName2}.nii.gz
>${FSL_FIXDIR}/training_files/HCP_hp2000.RData
>
>##MSMAllPipeline
>fMRINames="rfMRI_REST_Concat_Day1 rfMRI_REST_Concat_Day2"
>OutfMRIName="rfMRI_REST"
>HighPass="2000"
>fMRIProcSTRING="_Atlas_hp2000_clean"
>MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>RegName="MSMAll_InitalReg"
>HighResMesh="164"
>LowResMesh="32"
>InRegName="MSMSulc"
>MatlabMode="1"
>
>${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
>  --path=${StudyFolder} \
>  --subject=${Subject} \
>  --fmri-names-list=${fMRINames} \
>  --output-fmri-name=${OutfMRIName} \
>  --high-pass=${HighPass} \
>  --fmri-proc-string=${fMRIProcSTRING} \
>  --msm-all-templates=${MSMAllTemplates} \
>  --output-registration-name=${RegName} \
>  --high-res-mesh=${HighResMesh} \
>  --low-res-mesh=${LowResMesh} \
>  --input-registration-name=${InRegName} \
>  --matlab-run-mode=${MatlabMode}
>
>Thanks.
>
>Sang-Young
>
>
>
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[HCP-Users] MSMAll for MultiRunICAFIX

[Sang-Young Kim]

Dear Experts:

I have a question for MSMAll alignment for MultiRunICAFIX cleaned data. 
Once I run the MultiRunICAFIX pipeline, I get the output like 
"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii". 

But I want to align the data (e.g., 
${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii) using MSMAll pipeline. 
Running MSMAllPipeline script with above data seems to be fine without any 
error. However, if I run DeDriftAndResamplePipeline script, 
it requires ${fMRIConcatName}.${Hemisphere}.native.func.gii, which is absent in 
${fMRIConcatName} folder.

I can generate ${fMRIConcatName}.${Hemisphere}.native.func.gii using 
fMRISurfacePipeline. 
But I’m just wondering that I should run fMRISurfacePipeline for 
MultiRunICAFIX-cleaned data. 

This might be silly question as I don’t clearly understand MSMAllPipeline and 
DeDriftAndResamplePipeline. 
Is there a method to have MSMAll-aligned MultiRunICAFIX-cleaned data?

Below is the scripts that I ran:

## MultiRunICAFIX 
StudyFolder="/Volumes/easystore/projects/HCP"
Subject="300"
ConcatName1="rfMRI_REST_Concat_Day1"
ConcatName2="rfMRI_REST_Concat_Day2"
ResultFolder="${StudyFolder}/${Subject}/MNINonlinear/Results"
ICAFIXscriptFolder="/Users/sang-young/projects/Pipelines_master/ICAFIX"
 
${ICAFIXscriptFolder}/hcp_fix_multi_run 
${ResultFolder}/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz@${ResultFolder}/rfMRI_REST1_PA/rfMRI_REST1_PA.nii.gz@${ResultFolder}/rfMRI_REST2_AP/rfMRI_REST2_AP.nii.gz@${ResultFolder}/rfMRI_REST2_PA/rfMRI_REST2_PA.nii.gz
 2000 ${ResultFolder}/${ConcatName1}/${ConcatName1}.nii.gz 
${FSL_FIXDIR}/training_files/HCP_hp2000.RData

${ICAFIXscriptFolder}/hcp_fix_multi_run 
${ResultFolder}/rfMRI_REST3_AP/rfMRI_REST3_AP.nii.gz@${ResultFolder}/rfMRI_REST3_PA/rfMRI_REST3_PA.nii.gz@${ResultFolder}/rfMRI_REST4_AP/rfMRI_REST4_AP.nii.gz@${ResultFolder}/rfMRI_REST4_PA/rfMRI_REST4_PA.nii.gz
 2000 ${ResultFolder}/${ConcatName2}/${ConcatName2}.nii.gz 
${FSL_FIXDIR}/training_files/HCP_hp2000.RData

##MSMAllPipeline
fMRINames="rfMRI_REST_Concat_Day1 rfMRI_REST_Concat_Day2"
OutfMRIName="rfMRI_REST"
HighPass="2000"
fMRIProcSTRING="_Atlas_hp2000_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1"

${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
  --path=${StudyFolder} \
  --subject=${Subject} \
  --fmri-names-list=${fMRINames} \
  --output-fmri-name=${OutfMRIName} \
  --high-pass=${HighPass} \
  --fmri-proc-string=${fMRIProcSTRING} \
  --msm-all-templates=${MSMAllTemplates} \
  --output-registration-name=${RegName} \
  --high-res-mesh=${HighResMesh} \
  --low-res-mesh=${LowResMesh} \
  --input-registration-name=${InRegName} \
  --matlab-run-mode=${MatlabMode}

Thanks. 

Sang-Young



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Re: [HCP-Users] MSMAll

[Glasser, Matthew]

There are a couple of things that we need to sort out to make MSMAll work
with the new multi-run FIX code.  We will be working on that next week.

Matt.

On 10/5/18, 3:05 PM, "hcp-users-boun...@humanconnectome.org on behalf of
Shankar Tumati"  wrote:

>Hello,
>
>After running the hcp_fix_multi_run.sh script on the task data, a folder
>for concatenated files is created and a .ica folder is created in each
>task folder.
>
>However, MSMAllPipeline.sh script tries to find
>/filtered_func_data.ica/melodic_mix, which is present only in the Concat
>folder. When the script is run on the Concat folder, the output is a
>_MSMAll_hp2000_clean_vn.dtseries.nii file within a new output folder. Is
>this the correct output?
>
>Should we use the MSMAll.sh (not MSMAllpipeline.sh) instead and then
>apply DeDriftAndResamplePipeline.sh to get
>_MSMAll_hp2000_clean.dtseries.nii file for each task separately?
>
>Thank you
>
>Shankar Tumati
>
>Mind, Brain Imaging and Neuroethics lab
>University of Ottawa
>
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[HCP-Users] MSMAll

[Shankar Tumati]

Hello,

After running the hcp_fix_multi_run.sh script on the task data, a folder for 
concatenated files is created and a .ica folder is created in each task folder.

However, MSMAllPipeline.sh script tries to find 
/filtered_func_data.ica/melodic_mix, which is present only in the Concat 
folder. When the script is run on the Concat folder, the output is a 
_MSMAll_hp2000_clean_vn.dtseries.nii file within a new output folder. Is this 
the correct output?

Should we use the MSMAll.sh (not MSMAllpipeline.sh) instead and then apply 
DeDriftAndResamplePipeline.sh to get _MSMAll_hp2000_clean.dtseries.nii file for 
each task separately?

Thank you

Shankar Tumati

Mind, Brain Imaging and Neuroethics lab
University of Ottawa

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[HCP-Users] MSMAll

[Shankar Tumati]

Hello,

After running the hcp_fix_multi_run.sh script on the task data, a folder for 
concatenated files is created and a .ica folder is created in each task folder.

However, MSMAllPipeline.sh script tries to find 
/filtered_func_data.ica/melodic_mix, which is present only in the Concat 
folder. When the script is run on the Concat folder, the output is a 
_MSMAll_hp2000_clean_vn.dtseries.nii file within a new output folder. Is this 
the correct output?

Should we use the MSMAll.sh (not MSMAllpipeline.sh) instead and then apply 
DeDriftAndResamplePipeline.sh to get _MSMAll_hp2000_clean.dtseries.nii file for 
each task separately?

Thank you

Shankar Tumati

Mind, Brain Imaging and Neuroethics lab
University of Ottawa

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Re: [HCP-Users] MSMAll

[Glasser, Matthew]

We have not found that is necessary.  sICA+FIX worked on the HCP task data 
using the HCP resting state data training set.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Friday, July 27, 2018 at 3:15 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I noticed on the FSL FIX FAQ page the following:

Can I use FIX to clean task fMRI data?

  *   Yes, although you will probably need to create a study-specific training 
dataset

Can you speak to how multi run ICA+FIX gets away without needing a 
study-specific training dataset?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson 
mailto:hendr...@umn.edu>> wrote:
Sorry for the dumb question, I should have read the code further. Thanks!

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
The MR+FIX pipeline automatically breaks the runs back up at the end.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Tuesday, July 24, 2018 at 3:17 PM

To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

So once I finish with the multiICAFIX pipeline I wold have to manually separate 
the concatenated cleaned nifti file and then run MSMAll on those scans. Is that 
right?

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Give it a try, but you may find that you need to split it into two.  Make sure 
you are using the latest released FSL for this.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:26 PM

To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I handle processing for several studies, an upward bound for the studies I 
handle would be approximately 3000 frames.

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
FSL 6.0 hasn’t been released but has some updates to the math library that 
makes melodic much faster.  Also if you make too large of a merged file it will 
crash the old melodic because of some bugs.  How many frames are you wanting to 
do?

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:02 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of code 
there is a line with software requirements which include FIX >= 1.065 and FSL 
6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and 
melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure 
what melodic version would be considered equivalent "FSL 6.0". Could you shed 
some light on this for me?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>Fro

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

I noticed on the FSL FIX FAQ page the following:

Can I use FIX to clean task fMRI data?

   - Yes, although you will probably need to create a study-specific
   training dataset


Can you speak to how multi run ICA+FIX gets away without needing a
study-specific training dataset?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Tue, Jul 24, 2018 at 3:28 PM, Timothy Hendrickson 
wrote:

> Sorry for the dumb question, I should have read the code further. Thanks!
>
> Timothy Hendrickson
> Neuroimaging Analyst/Staff Scientist
> University of Minnesota Informatics Institute
> University of Minnesota
> Bioinformatics M.S. Candidate
> Office: 612-624-0783
> Mobile: 507-259-3434 (texts okay)
>
> On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew 
> wrote:
>
>> The MR+FIX pipeline automatically breaks the runs back up at the end.
>>
>> Matt.
>>
>> From: Timothy Hendrickson 
>> Date: Tuesday, July 24, 2018 at 3:17 PM
>>
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] MSMAll
>>
>> So once I finish with the multiICAFIX pipeline I wold have to manually
>> separate the concatenated cleaned nifti file and then run MSMAll on those
>> scans. Is that right?
>>
>> Timothy Hendrickson
>> Neuroimaging Analyst/Staff Scientist
>> University of Minnesota Informatics Institute
>> University of Minnesota
>> Bioinformatics M.S. Candidate
>> Office: 612-624-0783
>> Mobile: 507-259-3434 (texts okay)
>>
>> On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
>> wrote:
>>
>>> Give it a try, but you may find that you need to split it into two.
>>> Make sure you are using the latest released FSL for this.
>>>
>>> Matt.
>>>
>>> From: Timothy Hendrickson 
>>> Date: Monday, July 23, 2018 at 1:26 PM
>>>
>>> To: Matt Glasser 
>>> Cc: "hcp-users@humanconnectome.org" 
>>> Subject: Re: [HCP-Users] MSMAll
>>>
>>> I handle processing for several studies, an upward bound for the studies
>>> I handle would be approximately 3000 frames.
>>>
>>> Timothy Hendrickson
>>> Neuroimaging Analyst/Staff Scientist
>>> University of Minnesota Informatics Institute
>>> University of Minnesota
>>> Bioinformatics M.S. Candidate
>>> Office: 612-624-0783
>>> Mobile: 507-259-3434 (texts okay)
>>>
>>> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
>>> wrote:
>>>
>>>> FSL 6.0 hasn’t been released but has some updates to the math library
>>>> that makes melodic much faster.  Also if you make too large of a merged
>>>> file it will crash the old melodic because of some bugs.  How many frames
>>>> are you wanting to do?
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Timothy Hendrickson 
>>>> Date: Monday, July 23, 2018 at 1:02 PM
>>>> To: Matt Glasser 
>>>> Cc: "hcp-users@humanconnectome.org" 
>>>> Subject: Re: [HCP-Users] MSMAll
>>>>
>>>> Thanks Matt.
>>>>
>>>> With the hcp_fix_multi_run script I notice that in the first few lines
>>>> of code there is a line with software requirements which include FIX >=
>>>> 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have
>>>> FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me
>>>> I am not sure what melodic version would be considered equivalent "FSL
>>>> 6.0". Could you shed some light on this for me?
>>>>
>>>> -Tim
>>>>
>>>> Timothy Hendrickson
>>>> Neuroimaging Analyst/Staff Scientist
>>>> University of Minnesota Informatics Institute
>>>> University of Minnesota
>>>> Bioinformatics M.S. Candidate
>>>> Office: 612-624-0783
>>>> Mobile: 507-259-3434 (texts okay)
>>>>
>>>> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
>>>> wrote:
>>>>
>>>>> There is a new Multi-run FIX pipeline currently available in the Git
>>>>> repository that you can use.  I would consider it beta a this time.
>>>>>
>>>>> Matt.
>>>>>
>>>>> From:  on behalf of Timothy
>>>>> Hendrickson 
>&g

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

Sorry for the dumb question, I should have read the code further. Thanks!

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Tue, Jul 24, 2018 at 3:21 PM, Glasser, Matthew 
wrote:

> The MR+FIX pipeline automatically breaks the runs back up at the end.
>
> Matt.
>
> From: Timothy Hendrickson 
> Date: Tuesday, July 24, 2018 at 3:17 PM
>
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] MSMAll
>
> So once I finish with the multiICAFIX pipeline I wold have to manually
> separate the concatenated cleaned nifti file and then run MSMAll on those
> scans. Is that right?
>
> Timothy Hendrickson
> Neuroimaging Analyst/Staff Scientist
> University of Minnesota Informatics Institute
> University of Minnesota
> Bioinformatics M.S. Candidate
> Office: 612-624-0783
> Mobile: 507-259-3434 (texts okay)
>
> On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
> wrote:
>
>> Give it a try, but you may find that you need to split it into two.  Make
>> sure you are using the latest released FSL for this.
>>
>> Matt.
>>
>> From: Timothy Hendrickson 
>> Date: Monday, July 23, 2018 at 1:26 PM
>>
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] MSMAll
>>
>> I handle processing for several studies, an upward bound for the studies
>> I handle would be approximately 3000 frames.
>>
>> Timothy Hendrickson
>> Neuroimaging Analyst/Staff Scientist
>> University of Minnesota Informatics Institute
>> University of Minnesota
>> Bioinformatics M.S. Candidate
>> Office: 612-624-0783
>> Mobile: 507-259-3434 (texts okay)
>>
>> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
>> wrote:
>>
>>> FSL 6.0 hasn’t been released but has some updates to the math library
>>> that makes melodic much faster.  Also if you make too large of a merged
>>> file it will crash the old melodic because of some bugs.  How many frames
>>> are you wanting to do?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Timothy Hendrickson 
>>> Date: Monday, July 23, 2018 at 1:02 PM
>>> To: Matt Glasser 
>>> Cc: "hcp-users@humanconnectome.org" 
>>> Subject: Re: [HCP-Users] MSMAll
>>>
>>> Thanks Matt.
>>>
>>> With the hcp_fix_multi_run script I notice that in the first few lines
>>> of code there is a line with software requirements which include FIX >=
>>> 1.065 and FSL 6.0 melodic version. I have FIX version = 1.066 and I have
>>> FSL 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me
>>> I am not sure what melodic version would be considered equivalent "FSL
>>> 6.0". Could you shed some light on this for me?
>>>
>>> -Tim
>>>
>>> Timothy Hendrickson
>>> Neuroimaging Analyst/Staff Scientist
>>> University of Minnesota Informatics Institute
>>> University of Minnesota
>>> Bioinformatics M.S. Candidate
>>> Office: 612-624-0783
>>> Mobile: 507-259-3434 (texts okay)
>>>
>>> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
>>> wrote:
>>>
>>>> There is a new Multi-run FIX pipeline currently available in the Git
>>>> repository that you can use.  I would consider it beta a this time.
>>>>
>>>> Matt.
>>>>
>>>> From:  on behalf of Timothy
>>>> Hendrickson 
>>>> Date: Thursday, July 19, 2018 at 6:24 PM
>>>> To: "hcp-users@humanconnectome.org" 
>>>> Subject: [HCP-Users] MSMAll
>>>>
>>>> Hello,
>>>>
>>>> From the HCP course material I noticed that that suggested format to
>>>> use MSMAll is to do so immediately after the Minimal Pre-Processing stream
>>>> and immediately before subsequent tfMRI and rfMRI processing. As MSMAll
>>>> expects the data inputted to be run through ICA-FIX I am curious what I
>>>> should be doing with tfMRI data (i.e. what mods do I have to make to
>>>> hcp_fix, etc). If you could provide me a code snippet/s that would be 
>>>> great!
>>>>
>>>> -Tim
>>>>
>>>> Timothy Hendrickson
>>>> Neuroimaging Analyst/Staff Scientist
>>>> University of Minnesota Informatics Institute
>>>> Univers

Re: [HCP-Users] MSMAll

[Glasser, Matthew]

The MR+FIX pipeline automatically breaks the runs back up at the end.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Tuesday, July 24, 2018 at 3:17 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

So once I finish with the multiICAFIX pipeline I wold have to manually separate 
the concatenated cleaned nifti file and then run MSMAll on those scans. Is that 
right?

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
Give it a try, but you may find that you need to split it into two.  Make sure 
you are using the latest released FSL for this.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:26 PM

To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I handle processing for several studies, an upward bound for the studies I 
handle would be approximately 3000 frames.

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
FSL 6.0 hasn’t been released but has some updates to the math library that 
makes melodic much faster.  Also if you make too large of a merged file it will 
crash the old melodic because of some bugs.  How many frames are you wanting to 
do?

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:02 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of code 
there is a line with software requirements which include FIX >= 1.065 and FSL 
6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and 
melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure 
what melodic version would be considered equivalent "FSL 6.0". Could you shed 
some light on this for me?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>From the HCP course material I noticed that that suggested format to use 
>MSMAll is to do so immediately after the Minimal Pre-Processing stream and 
>immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects 
>the data inputted to be run through ICA-FIX I am curious what I should be 
>doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If 
>you could provide me a code snippet/s that would be great!

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

___
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

So once I finish with the multiICAFIX pipeline I wold have to manually
separate the concatenated cleaned nifti file and then run MSMAll on those
scans. Is that right?

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:31 PM, Glasser, Matthew 
wrote:

> Give it a try, but you may find that you need to split it into two.  Make
> sure you are using the latest released FSL for this.
>
> Matt.
>
> From: Timothy Hendrickson 
> Date: Monday, July 23, 2018 at 1:26 PM
>
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] MSMAll
>
> I handle processing for several studies, an upward bound for the studies I
> handle would be approximately 3000 frames.
>
> Timothy Hendrickson
> Neuroimaging Analyst/Staff Scientist
> University of Minnesota Informatics Institute
> University of Minnesota
> Bioinformatics M.S. Candidate
> Office: 612-624-0783
> Mobile: 507-259-3434 (texts okay)
>
> On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
> wrote:
>
>> FSL 6.0 hasn’t been released but has some updates to the math library
>> that makes melodic much faster.  Also if you make too large of a merged
>> file it will crash the old melodic because of some bugs.  How many frames
>> are you wanting to do?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Timothy Hendrickson 
>> Date: Monday, July 23, 2018 at 1:02 PM
>> To: Matt Glasser 
>> Cc: "hcp-users@humanconnectome.org" 
>> Subject: Re: [HCP-Users] MSMAll
>>
>> Thanks Matt.
>>
>> With the hcp_fix_multi_run script I notice that in the first few lines of
>> code there is a line with software requirements which include FIX >= 1.065
>> and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL
>> 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me I
>> am not sure what melodic version would be considered equivalent "FSL 6.0".
>> Could you shed some light on this for me?
>>
>> -Tim
>>
>> Timothy Hendrickson
>> Neuroimaging Analyst/Staff Scientist
>> University of Minnesota Informatics Institute
>> University of Minnesota
>> Bioinformatics M.S. Candidate
>> Office: 612-624-0783
>> Mobile: 507-259-3434 (texts okay)
>>
>> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
>> wrote:
>>
>>> There is a new Multi-run FIX pipeline currently available in the Git
>>> repository that you can use.  I would consider it beta a this time.
>>>
>>> Matt.
>>>
>>> From:  on behalf of Timothy
>>> Hendrickson 
>>> Date: Thursday, July 19, 2018 at 6:24 PM
>>> To: "hcp-users@humanconnectome.org" 
>>> Subject: [HCP-Users] MSMAll
>>>
>>> Hello,
>>>
>>> From the HCP course material I noticed that that suggested format to use
>>> MSMAll is to do so immediately after the Minimal Pre-Processing stream and
>>> immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects
>>> the data inputted to be run through ICA-FIX I am curious what I should be
>>> doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc).
>>> If you could provide me a code snippet/s that would be great!
>>>
>>> -Tim
>>>
>>> Timothy Hendrickson
>>> Neuroimaging Analyst/Staff Scientist
>>> University of Minnesota Informatics Institute
>>> University of Minnesota
>>> Bioinformatics M.S. Candidate
>>> Office: 612-624-0783
>>> Mobile: 507-259-3434 (texts okay)
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>> --
>>>
>>> The materials in this message are private and may contain Protected
>>> Healthcare Information or other information of a sensitive nature. If you
>>> are not the intended recipient, be advised that any unauthorized use,
>>> disclosure, copying or the taking of any action in reliance on the contents
>>> of this information is strictly prohibited. If you have received this email
>>> in error, please immediately notify the sender via telephone or return mail.
>>>
>>
>>
>> --
>>
>> The materials i

Re: [HCP-Users] MSMAll

[Glasser, Matthew]

Give it a try, but you may find that you need to split it into two.  Make sure 
you are using the latest released FSL for this.

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:26 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

I handle processing for several studies, an upward bound for the studies I 
handle would be approximately 3000 frames.

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
FSL 6.0 hasn’t been released but has some updates to the math library that 
makes melodic much faster.  Also if you make too large of a merged file it will 
crash the old melodic because of some bugs.  How many frames are you wanting to 
do?

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:02 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of code 
there is a line with software requirements which include FIX >= 1.065 and FSL 
6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and 
melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure 
what melodic version would be considered equivalent "FSL 6.0". Could you shed 
some light on this for me?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>From the HCP course material I noticed that that suggested format to use 
>MSMAll is to do so immediately after the Minimal Pre-Processing stream and 
>immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects 
>the data inputted to be run through ICA-FIX I am curious what I should be 
>doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If 
>you could provide me a code snippet/s that would be great!

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately not

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

I handle processing for several studies, an upward bound for the studies I
handle would be approximately 3000 frames.

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Mon, Jul 23, 2018 at 1:12 PM, Glasser, Matthew 
wrote:

> FSL 6.0 hasn’t been released but has some updates to the math library that
> makes melodic much faster.  Also if you make too large of a merged file it
> will crash the old melodic because of some bugs.  How many frames are you
> wanting to do?
>
> Peace,
>
> Matt.
>
> From: Timothy Hendrickson 
> Date: Monday, July 23, 2018 at 1:02 PM
> To: Matt Glasser 
> Cc: "hcp-users@humanconnectome.org" 
> Subject: Re: [HCP-Users] MSMAll
>
> Thanks Matt.
>
> With the hcp_fix_multi_run script I notice that in the first few lines of
> code there is a line with software requirements which include FIX >= 1.065
> and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL
> 5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me I
> am not sure what melodic version would be considered equivalent "FSL 6.0".
> Could you shed some light on this for me?
>
> -Tim
>
> Timothy Hendrickson
> Neuroimaging Analyst/Staff Scientist
> University of Minnesota Informatics Institute
> University of Minnesota
> Bioinformatics M.S. Candidate
> Office: 612-624-0783
> Mobile: 507-259-3434 (texts okay)
>
> On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
> wrote:
>
>> There is a new Multi-run FIX pipeline currently available in the Git
>> repository that you can use.  I would consider it beta a this time.
>>
>> Matt.
>>
>> From:  on behalf of Timothy
>> Hendrickson 
>> Date: Thursday, July 19, 2018 at 6:24 PM
>> To: "hcp-users@humanconnectome.org" 
>> Subject: [HCP-Users] MSMAll
>>
>> Hello,
>>
>> From the HCP course material I noticed that that suggested format to use
>> MSMAll is to do so immediately after the Minimal Pre-Processing stream and
>> immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects
>> the data inputted to be run through ICA-FIX I am curious what I should be
>> doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc).
>> If you could provide me a code snippet/s that would be great!
>>
>> -Tim
>>
>> Timothy Hendrickson
>> Neuroimaging Analyst/Staff Scientist
>> University of Minnesota Informatics Institute
>> University of Minnesota
>> Bioinformatics M.S. Candidate
>> Office: 612-624-0783
>> Mobile: 507-259-3434 (texts okay)
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MSMAll

[Glasser, Matthew]

FSL 6.0 hasn’t been released but has some updates to the math library that 
makes melodic much faster.  Also if you make too large of a merged file it will 
crash the old melodic because of some bugs.  How many frames are you wanting to 
do?

Peace,

Matt.

From: Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Monday, July 23, 2018 at 1:02 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of code 
there is a line with software requirements which include FIX >= 1.065 and FSL 
6.0 melodic version. I have FIX version = 1.066 and I have FSL 5.0.9 and 
melodic version 3.14. Without the FSL 6.0 release handy to me I am not sure 
what melodic version would be considered equivalent "FSL 6.0". Could you shed 
some light on this for me?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:
There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>From the HCP course material I noticed that that suggested format to use 
>MSMAll is to do so immediately after the Minimal Pre-Processing stream and 
>immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects 
>the data inputted to be run through ICA-FIX I am curious what I should be 
>doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If 
>you could provide me a code snippet/s that would be great!

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
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http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MSMAll

[Timothy Hendrickson]

Thanks Matt.

With the hcp_fix_multi_run script I notice that in the first few lines of
code there is a line with software requirements which include FIX >= 1.065
and FSL 6.0 melodic version. I have FIX version = 1.066 and I have FSL
5.0.9 and melodic version 3.14. Without the FSL 6.0 release handy to me I
am not sure what melodic version would be considered equivalent "FSL 6.0".
Could you shed some light on this for me?

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

On Thu, Jul 19, 2018 at 6:26 PM, Glasser, Matthew 
wrote:

> There is a new Multi-run FIX pipeline currently available in the Git
> repository that you can use.  I would consider it beta a this time.
>
> Matt.
>
> From:  on behalf of Timothy
> Hendrickson 
> Date: Thursday, July 19, 2018 at 6:24 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] MSMAll
>
> Hello,
>
> From the HCP course material I noticed that that suggested format to use
> MSMAll is to do so immediately after the Minimal Pre-Processing stream and
> immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects
> the data inputted to be run through ICA-FIX I am curious what I should be
> doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc).
> If you could provide me a code snippet/s that would be great!
>
> -Tim
>
> Timothy Hendrickson
> Neuroimaging Analyst/Staff Scientist
> University of Minnesota Informatics Institute
> University of Minnesota
> Bioinformatics M.S. Candidate
> Office: 612-624-0783
> Mobile: 507-259-3434 (texts okay)
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] MSMAll

[Glasser, Matthew]

There is a new Multi-run FIX pipeline currently available in the Git repository 
that you can use.  I would consider it beta a this time.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>>
Date: Thursday, July 19, 2018 at 6:24 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll

Hello,

>From the HCP course material I noticed that that suggested format to use 
>MSMAll is to do so immediately after the Minimal Pre-Processing stream and 
>immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects 
>the data inputted to be run through ICA-FIX I am curious what I should be 
>doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc). If 
>you could provide me a code snippet/s that would be great!

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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[HCP-Users] MSMAll

[Timothy Hendrickson]

Hello,

>From the HCP course material I noticed that that suggested format to use
MSMAll is to do so immediately after the Minimal Pre-Processing stream and
immediately before subsequent tfMRI and rfMRI processing. As MSMAll expects
the data inputted to be run through ICA-FIX I am curious what I should be
doing with tfMRI data (i.e. what mods do I have to make to hcp_fix, etc).
If you could provide me a code snippet/s that would be great!

-Tim

Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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Re: [HCP-Users] MSMAll data in HCP_1200 set

[Glasser, Matthew]

That isn’t the deformed sphere.  The spheres are in the Native folder and are 
GIFTI files.  They will have names like 
${Subject}.${Hemisphere}.sphere.MSMAll.surf.gii.  The template spheres will be 
in the 164k folder and have no MSMAll in them.  I would also recommend using 
the MSMAll midthickness surfaces for the resampling so that the vertex areas 
are appropriately handled.  Give a shot at constructing the command line and 
I’ll correct it if its wrong.

Peace,

Matt.

From: "Ho, Wilson Christopher" 
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:51 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll data in HCP_1200 set

Hi Matt,

Thank you for that explanation, it looks like 168038 and a few others are 
indeed missing the fMRI data, which would explain the missing files.

For the latter question (generating 164k Myelin Maps with MSMAll without BC), I 
found a post 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03480.html) 
where you advised using wb_command’s -cifti-resample. To clarify, the input 
CIFTI should be MyelinMap.164k_fs_LR.dscalar.nii, so should the template used 
be the SphericalDistortion_MSMAll.164k_fs_LR.dscalar.nii (aka the deformed 
sphere?)

Thanks again,

Wilson


From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Monday, January 22, 2018 at 2:19 PM
To: "Ho, Wilson Christopher" 
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] MSMAll data in HCP_1200 set

Are you using a group of subjects that had fMRI data?  They are required for 
MSMAll.  There should be 164k and 32k versions of the MSMAll aligned myelin 
maps.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Ho, Wilson Christopher" 
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:16 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll data in HCP_1200 set

Hello HCP experts,

I have a question about the MSMAll data. I know it’s advised to use the MSMAll 
variants of maps and surfaces for group analyses but some subjects are missing 
these (from what I’ve attempted to pull from the Amazon S3 database ). Take for 
example subject 168038, which has:

  *   168038.MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   168038.MyelinMap.164k_fs_LR.dscalar.nii
Missing however is a 168038.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii that a 
lot of other subjects have; this is the case with both 164k and 32k resolutions.
Next, does the 164k-resolution preclude MSMAll-only data? Many subjects have:

  *   MyelinMap.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
At the 32k resolution I notice they have the aforementioned, as well as a 
MyelinMap_MSMAll.32k_fs_LR.dscalar.nii (non-BC, MSM-only).

In these situations would it be advisable to run the analysis on what is 
available (eg. non-BC, non-MSMAll), or to reprocess these data (perhaps using 
the unprocessed versions) to obtain the missing files? Also, do we know if the 
data are yet to be added, or were they excluded due to other factors?

Thank you!

--
Wilson Ho

Programmer/Clinical Research Coordinator
MGH Center for Addiction Medicine
101 Merrimac St. Suite 320
Boston, MA 02114
Tel: 617-724-0367
w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>



The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [HCP-Users] MSMAll data in HCP_1200 set

[Ho, Wilson Christopher]

Hi Matt,

Thank you for that explanation, it looks like 168038 and a few others are 
indeed missing the fMRI data, which would explain the missing files.

For the latter question (generating 164k Myelin Maps with MSMAll without BC), I 
found a post 
(https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03480.html) 
where you advised using wb_command’s -cifti-resample. To clarify, the input 
CIFTI should be MyelinMap.164k_fs_LR.dscalar.nii, so should the template used 
be the SphericalDistortion_MSMAll.164k_fs_LR.dscalar.nii (aka the deformed 
sphere?)

Thanks again,

Wilson


From: "Glasser, Matthew" <glass...@wustl.edu>
Date: Monday, January 22, 2018 at 2:19 PM
To: "Ho, Wilson Christopher" <w...@mgh.harvard.edu>, 
"hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] MSMAll data in HCP_1200 set

Are you using a group of subjects that had fMRI data?  They are required for 
MSMAll.  There should be 164k and 32k versions of the MSMAll aligned myelin 
maps.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Ho, Wilson Christopher" 
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:16 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll data in HCP_1200 set

Hello HCP experts,

I have a question about the MSMAll data. I know it’s advised to use the MSMAll 
variants of maps and surfaces for group analyses but some subjects are missing 
these (from what I’ve attempted to pull from the Amazon S3 database ). Take for 
example subject 168038, which has:

  *   168038.MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   168038.MyelinMap.164k_fs_LR.dscalar.nii
Missing however is a 168038.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii that a 
lot of other subjects have; this is the case with both 164k and 32k resolutions.
Next, does the 164k-resolution preclude MSMAll-only data? Many subjects have:

  *   MyelinMap.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
At the 32k resolution I notice they have the aforementioned, as well as a 
MyelinMap_MSMAll.32k_fs_LR.dscalar.nii (non-BC, MSM-only).

In these situations would it be advisable to run the analysis on what is 
available (eg. non-BC, non-MSMAll), or to reprocess these data (perhaps using 
the unprocessed versions) to obtain the missing files? Also, do we know if the 
data are yet to be added, or were they excluded due to other factors?

Thank you!

--
Wilson Ho

Programmer/Clinical Research Coordinator
MGH Center for Addiction Medicine
101 Merrimac St. Suite 320
Boston, MA 02114
Tel: 617-724-0367
w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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Re: [HCP-Users] MSMAll data in HCP_1200 set

[Glasser, Matthew]

Are you using a group of subjects that had fMRI data?  They are required for 
MSMAll.  There should be 164k and 32k versions of the MSMAll aligned myelin 
maps.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Ho, Wilson Christopher" 
<w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>>
Date: Monday, January 22, 2018 at 1:16 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMAll data in HCP_1200 set

Hello HCP experts,

I have a question about the MSMAll data. I know it’s advised to use the MSMAll 
variants of maps and surfaces for group analyses but some subjects are missing 
these (from what I’ve attempted to pull from the Amazon S3 database ). Take for 
example subject 168038, which has:

  *   168038.MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   168038.MyelinMap.164k_fs_LR.dscalar.nii
Missing however is a 168038.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii that a 
lot of other subjects have; this is the case with both 164k and 32k resolutions.
Next, does the 164k-resolution preclude MSMAll-only data? Many subjects have:

  *   MyelinMap.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
At the 32k resolution I notice they have the aforementioned, as well as a 
MyelinMap_MSMAll.32k_fs_LR.dscalar.nii (non-BC, MSM-only).

In these situations would it be advisable to run the analysis on what is 
available (eg. non-BC, non-MSMAll), or to reprocess these data (perhaps using 
the unprocessed versions) to obtain the missing files? Also, do we know if the 
data are yet to be added, or were they excluded due to other factors?

Thank you!

--
Wilson Ho

Programmer/Clinical Research Coordinator
MGH Center for Addiction Medicine
101 Merrimac St. Suite 320
Boston, MA 02114
Tel: 617-724-0367
w...@mgh.harvard.edu<mailto:w...@mgh.harvard.edu>



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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[HCP-Users] MSMAll data in HCP_1200 set

[Ho, Wilson Christopher]

Hello HCP experts,

I have a question about the MSMAll data. I know it’s advised to use the MSMAll 
variants of maps and surfaces for group analyses but some subjects are missing 
these (from what I’ve attempted to pull from the Amazon S3 database ). Take for 
example subject 168038, which has:

  *   168038.MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   168038.MyelinMap.164k_fs_LR.dscalar.nii
Missing however is a 168038.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii that a 
lot of other subjects have; this is the case with both 164k and 32k resolutions.
Next, does the 164k-resolution preclude MSMAll-only data? Many subjects have:

  *   MyelinMap.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC.164k_fs_LR.dscalar.nii
  *   MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii
At the 32k resolution I notice they have the aforementioned, as well as a 
MyelinMap_MSMAll.32k_fs_LR.dscalar.nii (non-BC, MSM-only).

In these situations would it be advisable to run the analysis on what is 
available (eg. non-BC, non-MSMAll), or to reprocess these data (perhaps using 
the unprocessed versions) to obtain the missing files? Also, do we know if the 
data are yet to be added, or were they excluded due to other factors?

Thank you!

--
Wilson Ho

Programmer/Clinical Research Coordinator
MGH Center for Addiction Medicine
101 Merrimac St. Suite 320
Boston, MA 02114
Tel: 617-724-0367
w...@mgh.harvard.edu




The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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Re: [HCP-Users] MSMALL and areal classifier

[Glasser, Matthew]

MSMAll is already available in the HCP Pipelines repository and the MSM binary 
is here: https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/

We hope to make the areal classifier available in the future.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of 杨国元 <yangguoy...@pku.edu.cn<mailto:yangguoy...@pku.edu.cn>>
Date: Saturday, November 18, 2017 at 5:37 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] MSMALL and areal classifier

Hi,
  We want to use the multi-modal parcellation to produce a Chinese brain 
parcellation. We have already made the minimal preprocessing pipeline. Now we 
need the MSMALL and areal classifier to make the brain parcellation. So, where 
can I get these methods' source code?


Any suggestions?

Thanks!
Guoyuan


Guoyuan Yang
Center for MRI Research
School of Physics
Peking University
Beijing, China

Tel：18800172884
Email：yangguoy...@pku.edu.cn<mailto:Email：yangguoy...@pku.edu.cn>



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[HCP-Users] MSMALL and areal classifier

[杨国元]

Hi,
  We want to use the multi-modal parcellation to produce a Chinese brain 
parcellation. We have already made the minimal preprocessing pipeline. Now we 
need the MSMALL and areal classifier to make the brain parcellation. So, where 
can I get these methods' source code?



Any suggestions?


Thanks!
Guoyuan




Guoyuan Yang
Center for MRI Research
School of Physics
Peking University
Beijing, China


Tel：18800172884
Email：yangguoy...@pku.edu.cn




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Re: [HCP-Users] MSMALL atlas usage

[Timothy Coalson]

The surface outputs (label or metric) are in gifti format, and should be
named ending in .label.gii (for the -label case).  See "wb_command
-gifti-help".  Note that only the subcortical data is represented as voxels
(see "wb_command -cifti-help"), for which you should use the -volume-all
option to -cifti-separate.

Tim


On Tue, Aug 9, 2016 at 10:40 PM, A Nunes <adonay.s.nu...@gmail.com> wrote:

> Hi,
>
> Thanks for your replies. I tried to use wb_command -cifti-separate but I
> can't read the output with any toolbox.  I searched for examples in the HCP
> wiki but could not find a command example. The command I used for
> supposedly getting the right surface labels from the .dlabel.nii:
>
> wb_command -cifti-separate  /inpath/Q1-Q6_ReTest27.L.Cort
> icalAreas_dil_Final_Final_Individual.32k_fs_LR.dlabel.nii COLUMN   -label 
> CORTEX_RIGHT
> /outpath/Rlabel.nii
>
> Could you please tell me what I did wrong?
>
> Thanks
>
> Adonay
>
>
>
> On Tue, Aug 9, 2016 at 2:30 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>
>> Additionally, look at wb_command -cifti-separate to split the data into
>> formats that other tools can display (other formats are single-hemisphere
>> or voxel-only, so they can't contain all data of a cifti file in a single
>> file).
>>
>> Tim
>>
>>
>> On Tue, Aug 9, 2016 at 4:27 PM, Harms, Michael <mha...@wustl.edu> wrote:
>>
>>>
>>> Hi,
>>> If you want to visualize the parcellation, you will need to do that in
>>> Workbench.
>>>
>>> If you simply want to load the parcellation into Matlab for operations
>>> in which you treat each grayordinate as a numeric index, then see the
>>> following FAQ on the HCP Wiki page:
>>> https://wiki.humanconnectome.org/display/PublicData/HCP+User
>>> s+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave. Tel: 314-747-6173
>>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of A Nunes <
>>> adonay.s.nu...@gmail.com>
>>> Date: Tuesday, August 9, 2016 at 4:13 PM
>>> To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org>
>>> Subject: [HCP-Users] MSMALL atlas usage
>>>
>>> Hi,
>>>
>>> I would like to use this new MSMall atlas. For that  I need to open it
>>> in a toolbox or matlab, however I am not able to open it using either
>>>  freesurfer, caret, FSlviwer, fieldtrip, only through the workbench.
>>>
>>> So lets say I want to load this nii file in matlab using freesurfer
>>> MRIread: /BALSA/Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_ReTest/Q1-Q6_R
>>> eTest27/MNINonLinear/fsaverage_LR32k/Q1-Q6_ReTest27.R.Cortic
>>> alAreas_dil_Final_Final_Individual.32k_fs_LR.dlabel.nii
>>>
>>> Could you please explain me how to do it?
>>>
>>> Thanks
>>> Adonay
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>> --
>>>
>>> The materials in this message are private and may contain Protected
>>> Healthcare Information or other information of a sensitive nature. If you
>>> are not the intended recipient, be advised that any unauthorized use,
>>> disclosure, copying or the taking of any action in reliance on the contents
>>> of this information is strictly prohibited. If you have received this email
>>> in error, please immediately notify the sender via telephone or return mail.
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>

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Re: [HCP-Users] MSMALL atlas usage

[A Nunes]

Hi,

Thanks for your replies. I tried to use wb_command -cifti-separate but I
can't read the output with any toolbox.  I searched for examples in the HCP
wiki but could not find a command example. The command I used for
supposedly getting the right surface labels from the .dlabel.nii:

wb_command -cifti-separate  /inpath/Q1-Q6_ReTest27.L.
CorticalAreas_dil_Final_Final_Individual.32k_fs_LR.dlabel.nii COLUMN
  -label CORTEX_RIGHT /outpath/Rlabel.nii

Could you please tell me what I did wrong?

Thanks

Adonay



On Tue, Aug 9, 2016 at 2:30 PM, Timothy Coalson <tsc...@mst.edu> wrote:

> Additionally, look at wb_command -cifti-separate to split the data into
> formats that other tools can display (other formats are single-hemisphere
> or voxel-only, so they can't contain all data of a cifti file in a single
> file).
>
> Tim
>
>
> On Tue, Aug 9, 2016 at 4:27 PM, Harms, Michael <mha...@wustl.edu> wrote:
>
>>
>> Hi,
>> If you want to visualize the parcellation, you will need to do that in
>> Workbench.
>>
>> If you simply want to load the parcellation into Matlab for operations in
>> which you treat each grayordinate as a numeric index, then see the
>> following FAQ on the HCP Wiki page:
>> https://wiki.humanconnectome.org/display/PublicData/HCP+User
>> s+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
>>
>> cheers,
>> -MH
>>
>> --
>> Michael Harms, Ph.D.
>> ---
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave. Tel: 314-747-6173
>> St. Louis, MO  63110 Email: mha...@wustl.edu
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of A Nunes <
>> adonay.s.nu...@gmail.com>
>> Date: Tuesday, August 9, 2016 at 4:13 PM
>> To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org>
>> Subject: [HCP-Users] MSMALL atlas usage
>>
>> Hi,
>>
>> I would like to use this new MSMall atlas. For that  I need to open it in
>> a toolbox or matlab, however I am not able to open it using either
>>  freesurfer, caret, FSlviwer, fieldtrip, only through the workbench.
>>
>> So lets say I want to load this nii file in matlab using freesurfer
>> MRIread: /BALSA/Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_ReTest/Q1-Q6_R
>> eTest27/MNINonLinear/fsaverage_LR32k/Q1-Q6_ReTest27.R.
>> CorticalAreas_dil_Final_Final_Individual.32k_fs_LR.dlabel.nii
>>
>> Could you please explain me how to do it?
>>
>> Thanks
>> Adonay
>>
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Re: [HCP-Users] MSMALL atlas usage

[Timothy Coalson]

See entries 1 and 2 at
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ .

Tim


On Tue, Aug 9, 2016 at 4:13 PM, A Nunes  wrote:

> Hi,
>
> I would like to use this new MSMall atlas. For that  I need to open it in
> a toolbox or matlab, however I am not able to open it using either
>  freesurfer, caret, FSlviwer, fieldtrip, only through the workbench.
>
> So lets say I want to load this nii file in matlab using freesurfer
> MRIread: /BALSA/Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_ReTest/Q1-Q6_
> ReTest27/MNINonLinear/fsaverage_LR32k/Q1-Q6_ReTest27.R.CorticalAreas_dil_
> Final_Final_Individual.32k_fs_LR.dlabel.nii
>
> Could you please explain me how to do it?
>
> Thanks
> Adonay
>
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> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
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[HCP-Users] MSMALL atlas usage

[A Nunes]

Hi,

I would like to use this new MSMall atlas. For that  I need to open it in a
toolbox or matlab, however I am not able to open it using either
 freesurfer, caret, FSlviwer, fieldtrip, only through the workbench.

So lets say I want to load this nii file in matlab using freesurfer
MRIread:
/BALSA/Glasser_et_al_2016_HCP_MMP1.0_RVVG/HCP_ReTest/Q1-Q6_ReTest27/MNINonLinear/fsaverage_LR32k/Q1-Q6_ReTest27.R.CorticalAreas_dil_Final_Final_Individual.32k_fs_LR.dlabel.nii

Could you please explain me how to do it?

Thanks
Adonay

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